diff --git a/src/server.jl b/src/server.jl
index f1abab6..d4cc587 100644
--- a/src/server.jl
+++ b/src/server.jl
@@ -64,7 +64,14 @@ function _extract_timeout(merged_options)
 end
 
 function _exeflags_and_env(options)
-    exeflags = map(String, options["format"]["metadata"]["julia"]["exeflags"])
+    env_exeflags =
+        JSON3.read(get(ENV, "QUARTONOTEBOOKRUNNER_EXEFLAGS", "[]"), Vector{String})
+    options_exeflags = map(String, options["format"]["metadata"]["julia"]["exeflags"])
+    # We want to be able to override exeflags that are defined via environment variable,
+    # but leave the remaining flags intact (for example override number of threads but leave sysimage).
+    # We can do this by adding the options exeflags after the env exeflags.
+    # Julia will ignore earlier uses of the same flag.
+    exeflags = [env_exeflags; options_exeflags]
     env = map(String, options["format"]["metadata"]["julia"]["env"])
     # Use `--project=@.` if neither `JULIA_PROJECT=...` nor `--project=...` are specified
     if !any(startswith("JULIA_PROJECT="), env) && !any(startswith("--project="), exeflags)
@@ -537,11 +544,10 @@ end
 
 function default_frontmatter()
     D = Dict{String,Any}
-    exeflags = JSON3.read(get(ENV, "QUARTONOTEBOOKRUNNER_EXEFLAGS", "[]"), Vector{String})
     env = JSON3.read(get(ENV, "QUARTONOTEBOOKRUNNER_ENV", "[]"), Vector{String})
     return D(
         "fig-format" => "png",
-        "julia" => D("exeflags" => exeflags, "env" => env),
+        "julia" => D("env" => env, "exeflags" => []),
         "execute" => D("error" => true),
     )
 end
diff --git a/test/examples/exeflags_merging.qmd b/test/examples/exeflags_merging.qmd
new file mode 100644
index 0000000..a96cba2
--- /dev/null
+++ b/test/examples/exeflags_merging.qmd
@@ -0,0 +1,14 @@
+---
+title: Exeflags merging
+engine: julia
+julia:
+    exeflags: []
+---
+
+```{julia}
+print(Base.active_project())
+```
+
+```{julia}
+print(Threads.nthreads())
+```
\ No newline at end of file
diff --git a/test/testsets/exeflags_merging.jl b/test/testsets/exeflags_merging.jl
new file mode 100644
index 0000000..3aa51f7
--- /dev/null
+++ b/test/testsets/exeflags_merging.jl
@@ -0,0 +1,46 @@
+include("../utilities/prelude.jl")
+
+@testset "exeflags merging" begin
+
+    function with_replacement_file(f, file, replacements...)
+        s = read(file, String)
+        mktempdir() do dir
+            tempfile = joinpath(dir, basename(file))
+            open(tempfile, "w") do io
+                write(io, replace(s, replacements...))
+            end
+            f(tempfile)
+        end
+    end
+
+    file = joinpath(@__DIR__, "../examples/exeflags_merging.qmd")
+
+    withenv(
+        "QUARTONOTEBOOKRUNNER_EXEFLAGS" => "[\"--project=/set_via_env\", \"--threads=3\"]",
+    ) do
+        server = QuartoNotebookRunner.Server()
+        json = QuartoNotebookRunner.run!(server, file; showprogress = false)
+        @test contains(json.cells[2].outputs[1].text, "set_via_env")
+        @test json.cells[4].outputs[1].text == "3"
+        close!(server)
+
+        with_replacement_file(
+            file,
+            "[]" => "[\"--project=/override_via_frontmatter\"]",
+        ) do newfile
+            server = QuartoNotebookRunner.Server()
+            json = QuartoNotebookRunner.run!(server, newfile; showprogress = false)
+            @test contains(json.cells[2].outputs[1].text, "override_via_frontmatter")
+            @test json.cells[4].outputs[1].text == "3"
+            close!(server)
+        end
+
+        with_replacement_file(file, "[]" => "[\"--threads=5\"]") do newfile
+            server = QuartoNotebookRunner.Server()
+            json = QuartoNotebookRunner.run!(server, newfile; showprogress = false)
+            @test contains(json.cells[2].outputs[1].text, "set_via_env")
+            @test json.cells[4].outputs[1].text == "5"
+            close!(server)
+        end
+    end
+end